Methods and reagents for reducing non-specific amplification

ABSTRACT

The present invention provides methods and reagents for use in the amplification of nucleic acids. Amplification carried out using oligonucleotides containing modified nucleotides can result in less non-specific amplification compared to amplification carried out using unmodified oligonucleotides.

CROSS REFERENCE TO RELATED INVENTION

This application claims the benefit of U.S. Provisional PatentApplication Ser. No. 61/579,317, filed on Dec. 22, 2011, which isincorporated herein by reference in its entirety.

REFERENCE TO SEQUENCE LISTING

This application contains a Sequence Listing submitted as an electronictext file named “26108_US1_Sequence_Listing.txt”, having a size in bytesof 15 kb, and created on Dec. 10, 2012. The information contained inthis electronic file is hereby incorporated by reference in its entiretypursuant to 37 CFR §1.52(e)(5).

FIELD OF THE INVENTION

The present invention relates to the field of molecular biology andnucleic acid chemistry. More specifically it relates to methods andreagents for improving the reliability of nucleic acid amplificationreactions.

BACKGROUND OF THE INVENTION

The invention of the polymerase chain reaction (PCR) made possible thein vitro amplification of nucleic acid sequences. PCR is described inU.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188; Saiki et al., 1985,Science 230:1350-1354; Mullis et al., 1986, Cold Springs Harbor Symp.Quant. Biol. 51:263-273; and Mullis and Faloona, 1987, Methods Enzymol.155:335-350; each of which is incorporated herein by reference. Thedevelopment and application of PCR are described extensively in theliterature. For example, a range of PCR-related topics are discussed inPCR Technology—principles and applications for DNA amplification, 1989,(ed. H. A. Erlich) Stockton Press, New York; PCR Protocols: A guide tomethods and applications, 1990, (ed. M. A. Innis et al.) Academic Press,San Diego; and PCR Strategies, 1995, (ed. M. A. Innis et al.) AcademicPress, San Diego; each of which is incorporated herein by reference.Commercial vendors, such as Applied Biosystems (Foster City, Calif.),market PCR reagents and publish PCR protocols.

Since the original publication of nucleic acid amplification, variousprimer-based nucleic acid amplification methods have been describedincluding, but not limited to, the strand displacement assay (Walker etal., 1992, Proc. Natl. Acad. Sci. USA 89:392-396, Walker et al. 1992,Nucleic Acids Res. 20:1691-1696, and U.S. Pat. No. 5,455,166) and thetranscription-based amplification systems, including the methodsdescribed in U.S. Pat. Nos. 5,437,990; 5,409,818; and 5,399,491; thetranscription amplification system (TAS) (Kwoh et al., 1989, Proc. Natl.Acad. Sci. USA 86:1173-1177); and self-sustained sequence replication(3SR) (Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878and WO 92/08800). All of the above references are incorporated herein byreference. A survey of amplification systems is provided in Abramson andMyers, 1993, Current Opinion in Biotechnology 4:41-47, incorporatedherein by reference.

Specificity of primer-based amplification reactions largely depends onthe specificity of primer hybridization and extension. Under theelevated temperatures used in a typical amplification, the primershybridize only to the intended target sequence. However, amplificationreaction mixtures are typically assembled at room temperature, wellbelow the temperature needed to insure primer hybridization specificity.Under such less stringent conditions, the primers may bindnon-specifically to other only partially complementary nucleic acidsequences or to other primers and initiate the synthesis of undesiredextension products, which can be amplified along with the targetsequence. Amplification of non-specific primer extension products cancompete with amplification of the desired target sequences and cansignificantly decrease the efficiency of the amplification of thedesired sequence.

One frequently observed type of non-specific amplification product is atemplate-independent artifact of amplification reactions referred to as“primer dimer”. Primer dimer is a double-stranded fragment whose lengthtypically is close to the sum of the two primer lengths and appears tooccur when one primer is extended over the other primer. The resultingextension product forms an undesired template which, because of itsshort length, is amplified efficiently.

Non-specific amplification can be reduced by reducing the formation ofprimer extension products prior to the start of the reaction. In onemethod, referred to as a “hot-start” protocol, one or more criticalreagents are withheld from the reaction mixture until the temperature israised sufficiently to provide the necessary hybridization specificity.Manual hot-start methods, in which the reaction tubes are opened afterthe initial high temperature incubation step and the missing reagentsare added, are labor intensive and increase the risk of contamination ofthe reaction mixture. Alternatively, a heat sensitive material, such aswax, can be used to separate or sequester reaction components, asdescribed in U.S. Pat. No. 5,411,876, incorporated herein by reference,and Chou et al., 1992, Nucl. Acids Res. 20(7):1717-1723, incorporatedherein by reference. In these methods, a high temperature pre-reactionincubation melts the heat sensitive material, thereby allowing thereagents to mix.

Another method of reducing the formation of primer extension productsprior to the start of the reaction relies on the heat-reversibleinactivation of the DNA polymerase. U.S. Pat. Nos. 5,773,258 and5,677,152, both incorporated herein by reference, describe DNApolymerases reversibly modified by the covalent attachment of a modifiergroup. Incubation of the inactivated DNA polymerase at high temperatureresults in cleavage of the modifier-enzyme bond, thereby reactivatingthe enzyme.

Non-covalent reversible inhibition of a DNA polymerase by DNApolymerase-specific antibodies is described in U.S. Pat. Nos. 5,338,671,incorporated herein by reference.

Non-specific amplification also can be reduced by enzymaticallydegrading extension products formed prior to the start of the reactionusing the methods described in U.S. Pat. No. 5,418,149, which isincorporated herein by reference. The degradation of newly-synthesizedextension products is achieved by incorporating into the reactionmixture dUTP and UNG, and incubating the reaction mixture at 45-60° C.prior to carrying out the amplification reaction. Primer extensionresults in the formation of uracil-containing DNA, which is degraded byUNG under the pre-amplification conditions. A disadvantage of thismethod is that the degradation of extension product competes with theformation of extension product and the elimination of non-specificprimer extension product may be less complete. An advantage of thismethod is that uracil-containing DNA introduced into the reactionmixture as a contamination from a previous reaction is also degradedand, thus, the method also reduces the problem of contamination of a PCRby the amplified nucleic acid from previous reactions.

Another method of reducing the formation of primer extension productsprior to the start of the reaction relies on the use of primers modifiedat or near the 3′ end by the addition of a moiety to an exocyclic amine,as described in U.S. Pat. No. 6,001,611, incorporated herein byreference.

Conventional techniques of molecular biology and nucleic acid chemistry,which are within the skill of the art, are fully explained fully in theliterature. See, for example, Sambrook et al., 1989, Molecular Cloning—ALaboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor,N.Y.; Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Nucleic AcidHybridization (B. D. Hames and S. J. Higgins. eds., 1984); PCRTechnology—principles and applications for DNA amplification, 1989, (ed.H. A. Erlich) Stockton Press, New York; PCR Protocols: A guide tomethods and applications, 1990, (ed. M. A. Innis et al.) Academic Press,San Diego; and PCR Strategies, 1995, (ed. M. A. Innis et al.) AcademicPress, San Diego; all of which are incorporated herein by reference.

SUMMARY OF THE INVENTION

The present invention is based on the surprising discovery that incertain amplification reactions, particularly in reactions that containmultiple primers and probes for the amplification and detection ofmultiple target nucleic acids (e.g. multiplex PCR reactions), probe(s)can serve as a temple which could lead to non-specific amplificationwhich in turn would give the signal for false-positives. To reduce probebased non-specific amplification in PCR, minor groove modifiers whichinterferes with the activity of DNA polymerase but which is stillcapable of base pairing with a complementary nucleotide can be used. Onesuch example of a minor groove modifier is the deoxyguanosine analog,N²-benzyl guanosine (N²-benzyl-dG), which is the subject of the presentinvention as described herein.

Thus one aspect of the present invention relates to a method ofpreventing the extension by DNA polymerase of a primer oligonucleotidethat hybridizes to a template nucleotide sequence in an assay employingthe extension of a primer in a template-dependent manner comprising,incorporating a minor groove binder on the template nucleotide sequencewherein the primer oligonucleotide is incapable of being extended bymore than 2 nucleotides beyond the position of the minor groove binder.In one embodiment, the minor groove binder is a modified nucleoside. Inanother embodiment, the modified nucleoside is N²-benzyl-deoxyguanosine(N²-benzyl-dG).

Another aspect of the present invention relates to a method of reducingor preventing non-specific amplification of nucleic acid during anamplification reaction comprising providing at least one pair of primeroligonucleotides capable of amplifying a target nucleic acid sequence;providing a probe oligonucleotide that incorporates a minor groovebinder that blocks the extension of the primer oligonucleotide by a DNApolymerase by more than 2 nucleotides beyond the position of the minorgroove binder when the primer oligonucleotide hybridizes to the probeoligonucleotide. In one embodiment, the minor groove binder is amodified nucleoside. In another embodiment, the modified nucleoside isN²-benzyl-deoxyguanosine (N²-benzyl-dG).

A third aspect of the present invention relates to a reaction mixturefor the amplification of nucleic acids, comprising at least one pair ofprimer oligonucleotides and at least one probe oligonucleotide thatincorporates a N²-benzyl-dG nucleotide.

A fourth aspect of the present invention relates to a kit for theamplification of nucleic acids, comprising at least one pair of primeroligonucleotides, at least one probe oligonucleotide that incorporates aN²-benzyl-dG nucleotide, at least one nucleotide-incorporatingbiocatalyst, nucleoside triphosphates, a buffer suitable for theamplification of nucleic acids by the at least onenucleotide-incorporating biocatalyst, and a set of instructions forperforming the amplification of nucleic acids.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows (A) the structure of N²-benzyl-dG and (B) base pairingbetween N²-benzyl-dG and deoxycytosine (dC).

FIG. 2 is a graphic representation of the blocking of primer extensionusing a template nucleic acid containing N²-benzyl-dG.

FIG. 3 shows the results of the primer extension reaction of Example 1with A) No Enzyme, 0 min—Control Template, B) No Enzyme, 0min—NJS339_(—)1 Template, C) No Enzyme, 0 min—NJS339_(—)2A Template, D)5 min extension—Control Template, E) 5 min extension—NJS339_(—)1ATemplate, F) 5 min extension—NJS339_(—)2A Template.

FIG. 4 shows the melting temperatures of a complement oligonucleotideagainst three test oligonucleotides, one unmodified controloligonucleotide and two oligonucleotides with the identical sequence asthe control oligonucleotide but with N²-benzyl-dG modification at theN-4 or N-9 position.

FIG. 5 shows the cleavage efficiency of N²-benzyl-dG residue containingTaqMan® probes compared to unmodified TaqMan® probes with the identicalsequence where each probe targets the sequence from: A) HIV-1, B) HBV,C) HCV, D) HIV-2, and E) internal standard.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. In describing and claiming thepresent invention, the following definitions will be used.

The term “nucleic acid” refers to polymers of nucleotides (e.g.,ribonucleotides, deoxyribonucleotides, nucleotide analogs etc.) andcomprising deoxyribonucleic acids (DNA), ribonucleic acids (RNA),DNA-RNA hybrids, oligonucleotides, polynucleotides, aptamers, peptidenucleic acids (PNAs), PNA-DNA conjugates, PNA-RNA conjugates, etc., thatcomprise nucleotides covalently linked together, either in a linear orbranched fashion. A nucleic acid is typically single-stranded ordouble-stranded and will generally contain phosphodiester bonds,although in some cases, nucleic acid analogs are included that may havealternate backbones, including, for example, phosphoramide (Beaucage etal. (1993) Tetrahedron 49(10):1925); phosphorothioate (Mag et al. (1991)Nucleic Acids Res. 19:1437; and U.S. Pat. No. 5,644,048),phosphorodithioate (Briu et al. (1989) J. Am. Chem. Soc. 111:2321),O-methylphosphoroamidite linkages (see Eckstein, Oligonucleotides andAnalogues: A Practical Approach, Oxford University Press (1992)), andpeptide nucleic acid backbones and linkages (see, Egholm (1992) J. Am.Chem. Soc. 114:1895). Other analog nucleic acids include those withpositively charged backbones (Denpcy et al. (1995) Proc. Natl. Acad.Sci. USA 92: 6097); non-ionic backbones (U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863) and non-ribose backbones,including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506.Nucleic acids containing one or more carbocyclic sugars are alsoincluded within the definition of nucleic acids (see Jenkins et al.(1995) Chem. Soc. Rev. pp. 169-176), and analogs are also described in,e.g., Rawls, C & E News Jun. 2, 1997 page 35. These modifications of theribose-phosphate backbone may be done to facilitate the addition ofadditional moieties such as labels, or to alter the stability andhalf-life of such molecules in physiological environments.

In addition to the naturally occurring heterocyclic bases that aretypically found in nucleic acids (e.g., adenine, guanine, thymine,cytosine, and uracil), nucleotide analogs also may include non-naturallyoccurring heterocyclic bases, such as those described in, e.g., Seela etal. (1999) Hely. Chim. Acta 82:1640. Certain bases used in nucleotideanalogs act as melting temperature (Tm) modifiers. For example, some ofthese include 7-deazapurines (e.g., 7-deazaguanine, 7-deazaadenine,etc.), pyrazolo[3,4-d]pyrimidines, propynyl-dN (e.g., propynyl-dU,propynyl-dC, etc.), and the like. See, e.g., U.S. Pat. No. 5,990,303,which is incorporated herein by reference. Other representativeheterocyclic bases include, e.g., hypoxanthine, inosine, xanthine; 8-azaderivatives of 2-aminopurine, 2,6-diaminopurine, 2-amino-6-chloropurine,hypoxanthine, inosine and xanthine; 7-deaza-8-aza derivatives ofadenine, guanine, 2-aminopurine, 2,6-diaminopurine,2-amino-6-chloropurine, hypoxanthine, inosine and xanthine;6-azacytidine; 5-fluorocytidine; 5-chlorocytidine; 5-iodocytidine;5-bromocytidine; 5-methylcytidine; 5-propynylcytidine;5-bromovinyluracil; 5-fluorouracil; 5-chlorouracil; 5-iodouracil;5-bromouracil; 5-trifluoromethyluracil; 5-methoxymethyluracil;5-ethynyluracil; 5-propynyluracil, and the like.

A “nucleoside” refers to a nucleic acid component that comprises a baseor basic group (comprising at least one homocyclic ring, at least oneheterocyclic ring, at least one aryl group, and/or the like) covalentlylinked to a sugar moiety (a ribose sugar or a deoxyribose sugar), aderivative of a sugar moiety, or a functional equivalent of a sugarmoiety (e.g. a carbocyclic ring). For example, when a nucleosideincludes a sugar moiety, the base is typically linked to a 1′-positionof that sugar moiety. As described above, a base can be a naturallyoccurring base or a non-naturally occurring base. Exemplary nucleosidesinclude ribonucleosides, deoxyribonucleosides, dideoxyribonucleosidesand carbocyclic nucleosides.

A “nucleotide” refers to an ester of a nucleoside, e.g., a phosphateester of a nucleoside, having one, two, three or more phosphate groupscovalently linked to a 5′ position of a sugar moiety of the nucleoside.

A “purine nucleotide” refers to a nucleotide that comprises a purinebase, whereas a “pyrimidine nucleotide” refers to a nucleotide thatcomprises a pyrimidine base.

A “modified nucleotide” refers to rare or minor nucleic acid bases,nucleotides and modifications, derivations, or analogs of conventionalbases or nucleotides and includes synthetic nucleotides having modifiedbase moieties and/or modified sugar moieties (see, Protocols forOligonucleotide Conjugates, Methods in Molecular Biology, Vol. 26(Suhier Agrawal, Ed., Humana Press, Totowa, N.J., (1994)); andOligonucleotides and Analogues, A Practical Approach (Fritz Eckstein,Ed., IRL Press, Oxford University Press, Oxford); both incorporatedherein by reference.

An “oligonucleotide” refers to a nucleic acid polymer that includes atleast two, but typically 5-50 nucleotides and more typically, between 15and 35 nucleotides. The exact size of an oligonucleotide generallydepends on various factors, including the ultimate function or use ofthe oligonucleotide. Oligonucleotides may be prepared by any suitablemethod known in the art, including, for example, cloning and restrictiondigestion of appropriate sequences, or direct chemical synthesis by amethod such as the phosphotriester method of Narang et al. (1979) Meth.Enzymol. 68:90-99; the phosphodiester method of Brown et al. (1979)Meth. Enzymol. 68:109-151; the diethylphosphoramidite method of Beaucageet al. (1981) Tetrahedron Lett. 22:1859-1862; the triester method ofMatteucci et al. (1981) J. Am. Chem. Soc. 103:3185-3191; automatedsynthesis methods; the solid support method of U.S. Pat. No. 4,458,066or any other chemical method known in the art.

A “Watson-Crick base pairing” or simply “base pairing” refers to“conventional” hydrogen bonding within a double-stranded nucleic acidmolecule. Watson-Crick base pairing is hydrogen bonding between adenineand thymine, between guanine and cytosine, between adenine and uracil,and between analogs of these bases.

As used herein, the terms “hybridization” and “annealing” and the likeare used interchangeably and refer to the base-pairing interaction ofone polynucleotide with another polynucleotide (typically anantiparallel polynucleotide) that results in formation of a duplex orother higher-ordered structure, typically termed a hybridizationcomplex. The primary interaction between the antiparallel polynucleotidemolecules is typically base specific, e.g., A/T and G/C, by Watson/Crickand/or Hoogsteen-type hydrogen bonding. It is not a requirement that twopolynucleotides have 100% complementarity over their full length toachieve hybridization. In some aspects, a hybridization complex can formfrom intermolecular interactions, or alternatively, can form fromintramolecular interactions.

As used herein, the terms “amplification,” “amplifying” and the likerefer generally to any process that results in an increase in the copynumber of a molecule or set of related molecules. As it applies topolynucleotide molecules, amplification means the production of multiplecopies of a polynucleotide molecule, or a portion of a polynucleotidemolecule, typically starting from a small amount of a polynucleotide(e.g., a viral genome), where the amplified material (e.g., a viral PCRamplicon) is typically detectable. Amplification of polynucleotidesencompasses a variety of chemical and enzymatic processes. Thegeneration of multiple DNA copies from one or a few copies of a templateDNA molecule during a polymerase chain reaction (PCR), a stranddisplacement amplification (SDA) reaction, a transcription mediatedamplification (TMA) reaction, a nucleic acid sequence-basedamplification (NASBA) reaction, or a ligase chain reaction (LCR) areforms of amplification. Amplification is not limited to the strictduplication of the starting molecule. For example, the generation ofmultiple cDNA molecules from a limited amount of viral RNA in a sampleusing RT-PCR is a form of amplification. Furthermore, the generation ofmultiple RNA molecules from a single DNA molecule during the process oftranscription is also a form of amplification.

In some embodiments, amplification is optionally followed by additionalsteps, for example, but not limited to, labeling, sequencing,purification, isolation, hybridization, size resolution, expression,detecting and/or cloning.

As used herein, the term “polymerase chain reaction” (PCR) refers to amethod for amplification well known in the art for increasing theconcentration of a segment of a target polynucleotide in a sample, wherethe sample can be a single polynucleotide species, or multiplepolynucleotides. Generally, the PCR process consists of introducing amolar excess of two or more extendable oligonucleotide primers to areaction mixture comprising the desired target sequence(s), where theprimers are complementary to opposite strands of the double strandedtarget sequence. The reaction mixture is subjected to a program ofthermal cycling in the presence of a DNA polymerase, resulting in theamplification of the desired target sequence flanked by the DNA primers.Reverse transcriptase PCR (RT-PCR) is a PCR reaction that uses RNAtemplate and a reverse transcriptase, or an enzyme having reversetranscriptase activity, to first generate a single stranded DNA moleculeprior to the multiple cycles of DNA-dependent DNA polymerase primerelongation. Multiplex PCR refers to PCR reactions that produce more thanone amplified product in a single reaction, typically by the inclusionof more than two primers in a single reaction. Methods for a widevariety of PCR applications are widely known in the art, and describedin many sources, for example, Ausubel et al. (eds.), Current Protocolsin Molecular Biology, Section 15, John Wiley & Sons, Inc., New York(1994).

A “primer nucleic acid” or “primer” is an oligonucleotide that canhybridize to a template nucleic acid and permit chain extension orelongation using a nucleotide incorporating biocatalyst. Although otherprimer lengths are sometimes utilized, primers typically range from 15to 35 nucleotides. Short primer nucleic acids generally utilize coolertemperatures to form sufficiently stable hybrid complexes with templatenucleic acids. A primer nucleic acid that is at least partiallycomplementary to a subsequence of a template nucleic acid is typicallysufficient to hybridize with the template nucleic acid for extension tooccur. However, the success of the extension generally requires greatercomplementarity (i.e. fewer mismatches with the template) at the 3′-endof the primer. A primer nucleic acid can be labeled, if desired, byincorporating a label detectable by radiological, spectroscopic,photochemical, biochemical, immunochemical, or chemical techniques.

An “extended primer” refers to a primer to which one or more additionalnucleotides have been added. “Primer extension” is the action of theenzyme by which additional nucleotides are added to the primer.

A “template nucleic acid”, “template” or “target” refers to a nucleicacid to which a primer nucleic acid can hybridize and be extended undersuitable conditions. In the context of nucleic acid amplification,“target” is preferably a region of double stranded nucleic acid,consisting of the sequences at least partially complementary to at leasttwo primer sequences and the intervening sequence. A target can also bea single stranded nucleic acid, consisting of a sequence at leastpartially complementary to one primer and a sequence partially identicalto the second primer. Template nucleic acids can exist as isolatednucleic acid fragments or be a part of a larger nucleic acid fragment.Target nucleic acids can be derived or isolated from essentially anysource, such as cultured microorganisms, uncultured microorganisms,complex biological mixtures, tissues, sera, ancient or preserved tissuesor samples, environmental isolates or the like. Further, templatenucleic acids optionally include or are derived from cDNA, RNA, genomicDNA, cloned genomic DNA, genomic DNA libraries, enzymatically fragmentedDNA or RNA, chemically fragmented DNA or RNA, physically fragmented DNAor RNA, or the like. Template nucleic acids can also be chemicallysynthesized using techniques known in the art.

As used herein, the term “probe” refers typically to a polynucleotidethat is capable of hybridizing to a target nucleic acid of interest.Typically, but not exclusively, a probe is associated with a suitablelabel or reporter moiety so that the probe (and therefore its target)can be detected, visualized, measured and/or quantitated. Detectionsystems for labelled probes include, but are not limited to, thedetection of fluorescence, fluorescence quenching (e.g., when using aFRET pair detection system), enzymatic activity, absorbance, molecularmass, radioactivity, luminescence or binding properties that permitspecific binding of the reporter (e.g., where the reporter is anantibody). In some embodiments, a probe can be an antibody, rather thana polynucleotide, that has binding specificity for a nucleic acidnucleotide sequence of interest. It is not intended that the presentinvention be limited to any particular probe label or probe detectionsystem. The source of the polynucleotide used in the probe is notlimited, and can be produced synthetically in a non-enzymatic system, orcan be a polynucleotide (or a portion of a polynucleotide) that isproduced using a biological (e.g., enzymatic) system (e.g., in abacterial cell).

Typically, a probe is sufficiently complementary to a specific targetsequence contained in a nucleic acid to form a stable hybridizationcomplex with the target sequence under a selected hybridizationcondition, such as, but not limited to, a stringent hybridizationcondition. A hybridization assay carried out using the probe undersufficiently stringent hybridization conditions permits the selectivedetection of a specific target sequence.

As used herein, a primer is “specific” for a template sequence if thenumber of mismatches present between the primer sequence and the targetsequence is less than the number of mismatches present between theprimer sequence and non-target sequences which may be present in thesample. Hybridization conditions can be chosen under which stableduplexes are formed only if the number of mismatches present is no morethan the number of mismatches present between the primer sequence andthe target sequence. Under such conditions, the primer can form a stableduplex only with a target sequence. Thus, the use of target-specificprimers under suitably stringent amplification of those target sequenceswhich contain the target primer binding sites. The use ofsequence-specific amplification conditions enables the specificamplification of those target sequences which contain the exactlycomplementary primer binding sites.

The term “non-specific amplification” refers to the amplification ofnucleic acid sequences other than the target sequence which results fromprimers hybridizing to sequences other than the target sequence and thenserving as a substrate for primer extension. The hybridization of aprimer to a non-target sequence is referred to as “non-specifichybridization” and can occur during the lower temperature, reducedstringency, pre-amplification conditions.

As used herein, the term “amplicon” refers to a polynucleotide molecule(or collectively the plurality of molecules) produced following theamplification of a particular target nucleic acid. The amplificationmethod used to generate the amplicon can be any suitable method, mosttypically, for example, by using a PCR methodology. An amplicon istypically, but not exclusively, a DNA amplicon. An amplicon can besingle-stranded or double-stranded, or in a mixture thereof in anyconcentration ratio.

As used herein, the expression “real-time detection of ampliconaccumulation” refers to the detection of, and typically the quantitationthereof, of a specific amplicon or amplicons, as the amplicon(s) is/arebeing produced (typically by PCR) without the need for a detection orquantitation step following the completion of the amplification. Theterms “real-time PCR” or “kinetic PCR” refer to real-time detectionand/or quantitation of amplicon generated in a PCR.

A common method for real-time detection of amplicon accumulation is by a5′-nuclease assay, also termed a fluorogenic 5′-nuclease assay, e.g., aTaqMan analysis; see, Holland et al., Proc. Natl. Acad. Sci. USA88:7276-7280 (1991); and Heid et al., Genome Research 6:986-994 (1996).In the TaqMan PCR procedure, two oligonucleotide primers are used togenerate an amplicon specific to the PCR reaction. A thirdoligonucleotide (the TaqMan probe) is designed to hybridize with anucleotide sequence in the amplicon located between the two PCR primers.The probe may have a structure that is non-extendible by the DNApolymerase used in the PCR reaction, and is typically (but notnecessarily) colabeled with a fluorescent reporter dye and a quenchermoiety in close proximity to one another. The emission from the reporterdye is quenched by the quenching moiety when the fluor and quencher arein close proximity, as they are on the probe. In some cases, the probemay be labeled with only a fluorescent reporter dye or anotherdetectable moiety.

The TaqMan PCR reaction uses a thermostable DNA-dependent DNA polymerasethat possesses a 5′-3′ nuclease activity. During the PCR amplificationreaction, the 5′-3′ nuclease activity of the DNA polymerase cleaves thelabeled probe that is hybridized to the amplicon in a template-dependentmanner. The resultant probe fragments dissociate from theprimer/template complex, and the reporter dye is then free from thequenching effect of the quencher moiety. Approximately one molecule ofreporter dye is liberated for each new amplicon molecule synthesized,and detection of the unquenched reporter dye provides the basis forquantitative interpretation of the data, such that the amount ofreleased fluorescent reporter dye is directly proportional to the amountof amplicon template.

One measure of the TaqMan assay data is typically expressed as thethreshold cycle (CT). Fluorescence levels are recorded during each PCRcycle and are proportional to the amount of product amplified to thatpoint in the amplification reaction. The PCR cycle when the fluorescencesignal is first recorded as statistically significant, or where thefluorescence signal is above some other arbitrary level (e.g., thearbitrary fluorescence level, or AFL), is the threshold cycle (CT).

Protocols and reagents for 5′-nuclease assays are well known to one ofskill in the art, and are described in various sources. For example,5′-nuclease reactions and probes are described in U.S. Pat. No.6,214,979, entitled “HOMOGENEOUS ASSAY SYSTEM,” issued Apr. 10, 2001 toGelfand et al.; U.S. Pat. No. 5,804,375, entitled “REACTION MIXTURES FORDETECTION OF TARGET NUCLEIC ACIDS,” issued Sep. 8, 1998 to Gelfand etal.; U.S. Pat. No. 5,487,972, entitled “NUCLEIC ACID DETECTION BY THE5′-3′ EXONUCLEASE ACTIVITY OF POLYMERASES ACTING ON ADJACENTLYHYBRIDIZED OLIGONUCLEOTIDES,” issued Jan. 30, 1996 to Gelfand et al.;and U.S. Pat. No. 5,210,015, entitled “HOMOGENEOUS ASSAY SYSTEM USINGTHE NUCLEASE ACTIVITY OF A NUCLEIC ACID POLYMERASE,” issued May 11, 1993to Gelfand et al., all of which are incorporated by reference.

Variations in methodologies for real-time amplicon detection are alsoknown, and in particular, where the 5′-nuclease probe is replaced bydouble-stranded DNA intercalating dye resulting in fluorescence that isdependent on the amount of double-stranded amplicon that is present inthe amplification reaction. See, for example, U.S. Pat. No. 6,171,785,entitled “METHODS AND DEVICES FOR HEMOGENEOUS NUCLEIC ACID AMPLIFICATIONAND DETECTOR,” issued Jan. 9, 2001 to Higuchi; and U.S. Pat. No.5,994,056, entitled “HOMOGENEOUS METHODS FOR NUCLEIC ACID AMPLIFICATIONAND DETECTION,” issued Nov. 30, 1999 to Higuchi, each of which areincorporated by reference.

TaqMan® PCR can be performed using commercially available kits andequipment, such as, for example, ABI PRISM® 7700 Sequence DetectionSystem (Applied Biosystems, Foster City, Calif.), or LightCycler® (RocheApplied Sciences, Mannheim, Germany). In a preferred embodiment, the 5′nuclease assay procedure is run on a real-time quantitative PCR devicesuch as the ABI PRISM® 7700 Sequence Detection System. The systemconsists of a thermocycler, laser, charge-coupled device (CCD), cameraand computer. The system amplifies samples in a 96-well microtiter plateformat on a thermocycler. During amplification, laser-inducedfluorescent signal is collected in real-time through fiber optics cablesfor all 96 wells, and detected at the CCD camera. The system includessoftware for running the instrument and for analyzing the data.

As used herein, a “gene” refers to any segment of DNA associated with abiological function. Thus, genes include coding sequences andoptionally, the regulatory sequences required for the expression of thecoding sequences.

Nucleic acids are “extended” or “elongated” when additional nucleotidesare incorporated into the nucleic acids, for example by a nucleotideincorporating biocatalyst, at the 3′ end of a nucleic acid.

A “moiety” or “group” refers to one of the portions into whichsomething, such as a molecule, is divided (e.g., a functional group,substituent group, or the like). For example, a nucleotide typicallycomprises a base group (e.g., adenine, thymine, cytosine, guanine,uracil, or an analog), a sugar moiety, and one or more phosphate groups.

A “benzyl group” refers a monovalent aromatic group with the formulaC₆H₅CH₂— and is used interchangeably with the term “phenylmethyl”.

A “genotype” refers to all or part of the genetic constitution of a cellor subject, or group of cells or subjects. For example, a genotypeincludes the particular mutations and/or alleles (e.g. polymorphisms,such as single nucleotide polymorphisms (SNPs) or the like) present at agiven locus or distributed in a genome. “Genotyping” refers to an assaythat determines the genotype of a cell or subject.

A “nucleotide incorporating biocatalyst” or “nucleotide incorporatingenzyme” refers to a catalyst (or enzyme) that catalyzes theincorporation of nucleotides into a nucleic acid. Exemplary nucleotideincorporating enzymes include, DNA polymerases, RNA polymerases,terminal transferases, reverse transcriptases, telomerases and the like.

A “thermostable enzyme” refers to an enzyme that is stable (i.e.,resists breakdown or denaturation) and retains sufficient catalyticactivity when subjected to elevated temperatures for selected periods oftime. For example, a thermostable polymerase retains sufficient activityto effect subsequent primer extension reactions, when subjected toelevated temperatures for the time necessary to denature double-strandednucleic acids. Heating conditions necessary for nucleic aciddenaturation are well known in the art and are exemplified in U.S. Pat.Nos. 4,683,202 and 4,683,195. As used herein, a thermostable polymeraseis typically suitable for use in a temperature cycling reaction such asthe polymerase chain reaction (“PCR”). The examples of thermostablenucleic acid polymerases include Thermus aquaticus Taq DNA polymerase,Thermus sp. Z05 polymerase, Thermus flavus polymerase, Thermotogamaritima polymerases, such as TMA-25 and TMA-30 polymerases, Tth DNApolymerase, and the like.

A “modified enzyme” refers to an enzyme comprising an amino acid polymerin which at least one monomer differs from the reference sequence, suchas a native or wild-type form of the enzyme or another modified form ofthe enzyme. Exemplary modifications include monomer insertions,deletions, and substitutions. Modified enzymes also include chimericenzymes that have identifiable component sequences (e.g., structural orfunctional domains, etc.) derived from two or more parents. Alsoincluded within the definition of modified enzymes are those comprisingchemical modifications of the reference sequence. The examples ofmodified polymerases include G46E E678G CS5 DNA polymerase, G46E L329AE678G CS5 DNA polymerase, G46E L329A D640G S671F CS5 DNA polymerase,G46E L329A D640G S671F E678G CS5 DNA polymerase, a G46E E678G CS6 DNApolymerase, ΔZ05 polymerase, ΔZ05-Gold polymerase, ΔZ05R polymerase,E615G Taq DNA polymerase, E678G TMA-25 polymerase, E678G TMA-30polymerase, and the like.

The term “5′ to 3′ nuclease activity” or “5′-3′ nuclease activity”refers to an activity of a nucleic acid polymerase, typically associatedwith the nucleic acid strand synthesis, whereby nucleotides are removedfrom the 5′ end of nucleic acid strand, e.g., E. coli DNA polymerase Ihas this activity, whereas the Klenow fragment does not.

A polymerase that “substantially lacks 5′-3′ nuclease activity” refersto a polymerase that has 50% or less (e.g., <25%, <20%, <15%, <10%)5′-3′ nuclease activity than Taq DNA polymerase. Methods of measuring5′-3′ nuclease activity and conditions for measurement are well known inthe art. See, e.g., U.S. Pat. No. 5,466,591. Examples of DNA polymerasessubstantially lacking 5′ to 3′ nuclease activity include the Klenowfragment of E. coli DNA polymerase I; a Thermus aquaticus DNA polymerase(Taq) lacking the N-terminal 235 amino acids (e.g., as described in U.S.Pat. No. 5,616,494 and commonly referred to in the art as the “Stoffelfragment”). Other examples include a thermostable DNA polymerase havingsufficient deletions (e.g., N-terminal deletions), mutations, ormodifications so as to eliminate or inactivate the domain responsiblefor the 5′-3′ nuclease activity. See, e.g., U.S. Pat. No. 5,795,762.

A “label” refers to a moiety attached (covalently or non-covalently), toa molecule and capable of providing information about the molecule.Exemplary labels include fluorescent labels, colorimetric labels,chemiluminescent labels, bioluminescent labels, radioactive labels,mass-modifying groups, antibodies, antigens, biotin, haptens, andenzymes (including peroxidase, phosphatase, etc.).

A “hot start”, in the context of a nucleic acid amplification reaction,refers to a protocol, where at least one critical reagent is withheldfrom the reaction mixture (or, if present in the reaction mixture, thereagent remains inactive) until the temperature is raised sufficientlyto provide the necessary hybridization specificity of the primer orprimers. A “hot start enzyme” is an enzyme, typically a nucleic acidpolymerase, capable of acting as the “withheld” or inactive reagent in ahot start protocol.

The term “reaction mixture” refers to a solution containing reagentsnecessary to carry out a given reaction. An “amplification reactionmixture”, which refers to a solution containing reagents necessary tocarry out an amplification reaction, typically contains oligonucleotideprimers and a DNA polymerase or ligase in a suitable buffer. A “PCRreaction mixture” typically contains oligonucleotide primers, athermostable DNA polymerase dNTP's, and a divalent metal cation in asuitable buffer. A reaction mixture is referred to as complete if itcontains all reagents necessary to enable the reaction, and incompleteif it contains only a subset of the necessary reagents. It will beunderstood by one of skill in the art that reaction components areroutinely stored as separate solutions, each containing a subset of thetotal components, for reasons of convenience, storage, stability, or toallow for application-dependent adjustment of the componentconcentrations, and, that reaction components are combined prior to thereaction to create a complete reaction mixture.

As used herein, the term “kit” is used in reference to a combination ofarticles that facilitate a process, method, assay, analysis ormanipulation of a sample. Kits can contain written instructionsdescribing how to use the kit (e.g., instructions describing the methodsof the present invention), chemical reagents or enzymes required for themethod, primers and probes, as well as any other components.

The present invention is based on the discovery that certain modifiednucleotides, when present on a template nucleic acid, are able toprevent or inhibit the extension of a primer oligonucleotide by DNApolymerase but can still maintain Watson-Crick base pairing with itscomplementary base on the primer. One such modified nucleotide is thedeoxyguanosine analog, N²-benzyl-deoxyguanosine (N²-benzyl-dG) which, asshown on FIG. 1A, contains a benzyl group on the C-2 nitrogen of theexocyclic amino group. The nucleotides with covalent modifications ofthe exocyclic amino groups have been described in U.S. Pat. No.6,001,611, which is incorporated herein by reference. The synthesis ofsuch nucleotides, and oligonucleotides incorporating such nucleotidesare also described in the '611 patent.

While not being constrained by the theory, it is believed thatN²-benzyl-dG is able to prevent primer extension by occupying the minorgroove of double-stranded DNA, thereby behaving as a “minor groovebinder” and interfering with the active site of the DNA polymerase.Nevertheless, base pairing with a complementary deoxycytosine (dC)nucleotide can still occur as the three hydrogen bonds are not affectedby the presence of the benzyl moiety (FIG. 1B).

Therefore, in one aspect, the present invention relates to a method ofpreventing the extension by DNA polymerase of a primer oligonucleotidethat hybridizes to a template nucleotide sequence, comprisingincorporating a minor groove binder on the template nucleotide sequencewherein the minor groove binder is a modified nucleotide and themodified nucleotide is N²-benzyl-dG and wherein the primer is incapableof being extended by more than 2 nucleotides beyond the position of theN²-benzyl-dG nucleotide. This method would be applicable for theperformance of PCR amplification, nucleic acid sequencing, genotyping,and other applications employing the extension of a primer in atemplate-dependent manner.

The unique properties of N²-benzyl-dG would also allow for its use inthe reduction or prevention of non-specific amplification in aprimer-based amplification reaction. It is believed that non-specificamplification occurs when an unstable, transient hybridization duplex isformed between a primer and a non-target molecule, in which the 3′ endof the primer is momentarily paired with a complementary base in theother molecule. Initial primer extension results in the formation ofcomplementary sequence which stabilizes the duplex and allows forfurther extension. U.S. Pat. No. 6,011,611 discloses the use of primerscontaining modified nucleotides for preventing non-specificamplification that results from the formation of primer-dimers in whichthe transient hybridization duplex is formed between a primer andanother primer. N²-benzyl-dG would not be utilized in a primer toprevent non-specific amplification because its presence in primerextension products which are used as templates in subsequentamplification cycles would cause the termination of primer extension.However, in amplification reactions that utilize a probe (for example a5′ nuclease probe in the Taqman PCR assay) incorporation of N²-benzyl-dGhas resulted in reducing or preventing non-specific amplification thatresults from hybridization taking place between a primer and a probe.

Therefore, in another aspect, the present invention relates to a methodof reducing or preventing non-specific amplification of nucleic acidduring an amplification reaction comprising providing at least one pairof primer oligonucleotides capable of amplifying a target nucleic acidsequence; providing a probe oligonucleotide that incorporates a minorgroove binder that blocks the extension of the primer by a DNApolymerase by more than 2 nucleotides beyond the position of the minorgroove binder when the primer hybridizes to the probe oligonucleotide.In one embodiment, the minor groove binder is a modified nucleotide. Inanother embodiment, the modified nucleotide is N²-benzyl-dG.

In another aspect, the invention provides a reaction mixture for theamplification of nucleic acids, comprising at least one pair of primeroligonucleotides and at least one probe oligonucleotide thatincorporates a N²-benzyl-dG nucleotide. In some embodiments, thereaction mixture further comprises the reagents and solutions generallynecessary for the amplification of nucleic acids, including anucleotide-incorporating biocatalyst, nucleic acid precursors, i.e.nucleoside triphosphates, and organic and inorganic ions, suitable forthe support of the activity of the nucleotide-incorporating biocatalyst.

In another aspect, the invention provides kits for conducting theamplification reaction according to the invention. The kit generallyincludes assay-specific components as well as components generallyrequired for performing DNA amplification assays. As the assay-specificcomponents, the amplification kit of the present invention typicallyincludes at least one pair of primer oligonucleotides, at least oneprobe oligonucleotide that incorporates a N²-benzyl-dG nucleotide, and aset of instructions for conducting the amplification reaction of thepresent invention. In some embodiments, the kit includes two or morepairs of primer oligonucleotides and two or more probe oligonucleotideswherein each probe oligonucleotide incorporates a N²-benzyl-dGnucleotide. As the components generally required for nucleic acidamplification, the kit of the present invention typically includes oneor more of a nucleotide incorporating biocatalyst, nucleic acidprecursors, such as nucleoside triphosphates (deoxyribonucleosidetriphosphates or ribonucleoside triphosphates), optionally, apyrophosphatase, for minimizing pyrophosphorolysis of nucleic acids, auracil N-glycosylase (UNG) for protection against carry-overcontamination of amplification reactions, and pre-made reagents andbuffers necessary for the amplification reaction and detection.

The following examples and figures are provided to aid the understandingof the present invention, the true scope of which is set forth in theappended claims. It is understood that modifications can be made in theprocedures set forth without departing from the spirit of the invention.

EXAMPLES Example 1 Primer Extension

In order to demonstrate that a template nucleic acid containingN²-benzyl-dG is able to block the extension of a primer by DNApolymerase as graphically depicted in FIG. 2, a primer extensionexperiment was set up using a FAM-labeled primer oligonucleotide andthree complementary template oligonucleotides with sequences that areshown below:

(SEQ ID NO: 1) NJS01 FAM-CCCTCGCAGCCGTCCAACCAACTCA (SEQ ID NO: 2) NJS03    GGGAGCGTCGGCAGGTTGGTTGAGTAGGTCTTGTTT (SEQ ID NO: 3) NJS339-    CGGAGCGTCGGCAGGTTGGTTGAGTAGETCTTGTTT 1A (SEQ ID NO: 4) NJS339-    CGGAGCGTCGGCAGGTTGGTTGAGTAGGTCTTETTT 2A (E = N²-benzyl-dG)

Each primer extension reaction (50 μl) contained 50 nM primer and 75 nMtemplate oligonucleotide, with 15 units (20 nM) Z05D DNA polymerase,337.5 μM each dATP, dCTP, dGTP, dUTP, 50 mM Tricine (pH 8.0), 100 mMpotassium acetate (pH 7.0), 3 mM manganese acetate, 4% glycerol, 5%DMSO, 0.01% Tween-20. Primer extension with Z05D DNA polymerase wasperformed at 60° C. and the reaction was terminated by the addition ofEDTA at various time points. The primer extension products were dilutedinto loading buffer with formamide and were analyzed by capillaryelectrophoresis (ABI PRISM® 3100 Genetic Analyzer) in the presence oflabeled size standards.

The results are shown on FIG. 3. The extension products from thetemplates that contain N²-benzyl-dG are clearly smaller than theextension product from the control template. This indicates that atemplate nucleic acid that contains a N²-benzyl-dG residue can stop ordramatically reduce the extension rate of a primer by DNA polymerase.

Example 2 Duplex Stability

To study the effect of N²-benzyl-dG on hybridization, a meltingtemperature experiment was performed using an unmodified complementoligonucleotide and three test oligonucleotides. The three testoligonucleotides for which melting temperatures were determinedrepresent (a) an unmodified control oligonucleotide, (b) anoligonucleotide with identical sequence as (a) with N²-benzyl-dG at theN-9 position, and (c) an oligonucleotide with identical sequence as (a)with N²-benzyl-dG at the N-4 position. The nucleotide sequences of theseoligonucleotides are as follows:

(SEQ ID NO: 5) Comple- 3′-AAACAAGACCTACTCAACCAACCTGCCGACGCTCCG ment(SEQ ID NO: 6) Test  5′-TTTGTTCTGGATGAGTTGGTTGGACGGCTGCGAGGC Control(SEQ ID NO: 7) Test N-9 5′-TTTGTTCTEGATGAGTTGGTTGGACGGCTGCGAGGC(SEQ ID NO: 8) Test N-4 5′-TTTETTCTGGATGAGTTGGTTGGACGGCTGCGAGGC

The experimental conditions were as follows. Each reaction was preparedin 500 volume and in replicates of two and contained 40 pmol of eachtest oligonucleotide and 40 pmol of complement oligonucleotide, in abuffer that contained 90 mM potassium acetate (pH 7.0), 50 mM Tricine(pH 8.3), 3 mM manganous acetate, 3% glycerol, 5% DMSO, 300 μM each ofdATP, dCTP, dGTP and 600 μM dUTP. The melting temperature for thehybridization duplex formed between each test oligonucleotide and thecomplement oligonucleotide was determined using the LighCycler® 480Instrument under the following conditions. Each reaction well as firstheated to 91° C. and rapidly cooled to 40° C. to allow annealing to takeplace. Temperature was then continuously raised at a ramp rate of 0.06°C./sec to 90° C. Detection of DNA duplex melting was via the change influorescence by the double-stranded DNA-binding dye Syto-13 (finalconcentration 100 μM).

The results of the experiment are shown on FIG. 4 with the top panelshowing absolute fluorescence plotted as a function of temperature andthe bottom panel depicting the same melting curve data but displayingthe data as a first derivative plot (as a function of temperature). Onlya small melting temperature difference was observed between the controloligonucleotide and the oligonucleotides containing N²-benzyl-dG withΔTm values of 0.3° C.-0.5° C. Thus the presence of N²-benzyl-dG in anoligonucleotide does not lead to significant destabilization of ahybridization duplex formed between the N²-benzyl-dG-containingoligonucleotide and a complementary nucleic acid sequence. Thisexperiment demonstrates that N²-benzyl-dG can be incorporated within aprobe oligonucleotide (e.g. a TaqMan® probe) without adversely affectingthe hybridization property of the probe.

Example 3 Cleavage Efficiency

To investigate whether a 5′-nuclease oligonucleotide probe that containsN²-benzyl-dG can be effectively cleaved by the 5′ to 3′ nucleaseactivity of DNA polymerase in a TaqMan® PCR assay, the followingexperiment was performed. TaqMan® probes that target specific viralsequences in HIV-1, HIV-2, HBV, and HCV were modified to contain oneresidue of N²-benzyl-dG. Each of the modified TaqMan® probes was thencompared with its counterpart unmodified TaqMan® probe in a standardkinetic PCR assay using target-specific primers and Z05 DNA polymerasefor its amplicon-detection ability which indicates how effectively theprobe are cleaved by the 5′ to 3′ nuclease activity of the DNApolymerase.

The results are shown on FIG. 5 as represented by growth curves for eachPCR reaction with fluorescence plotted against PCR cycle number. Foreach target, there is little or no difference between the growth curvesgenerated using N²-benzyl-dG-modified TaqMan® probes and those usingunmodified TaqMan® probes. This demonstrates that the cleavageefficiency by DNA polymerase of N²-benzyl-dG containing TaqMan® probesis the same as that of a TaqMan® probe that does not containN²-benzyl-dG.

Example 4 Reduction of False Positives

During a multiplex PCR assay, it was observed that false positive dataas a result of non-specific amplification appeared in a channel thatcontained a HCV-specific TaqMan® probe labeled with the fluorescentJA270 dye. As shown in Table 1, incorporation of N²-benzyl-dG in the HCVTaqMan® probe was able to eliminate the presence of the false positivesignal in the JA270 channel (Channel 3).

TABLE 1 Unexpected Reactives Samples (False Positives) Summary MatrixReplicates Channel 3 Overall Control Probes NHP 120 3 3% Benzyl-dG NHP120 0 0% probes

Example 5 Reduction of False Positives in a Multiplex PCR Assay

In order to show the potential of N²-benzyl-dG modification of TaqMan®probes as a means to reduce false positivity, an experiment was run inwhich the false positivity rate was measured using conventional probesand those with N²-benzyl-dG at specific locations within the probesequences. Since false positivity is relatively infrequent in highlyoptimized amplification systems, a modified PCR Master Mix was developedwhich favored the generation of non-specific amplification products. Inthis model system, a high level of false positivity could be inducedsuch that a statistically significant difference between the rates wouldbe obvious from a relatively limited number of input samples.

Samples of Normal Human Plasma (NHP, 850 μl each, N=388 for eachcondition tested) which had been previously confirmed as being negativefor the viruses to be detected, Human Immunodeficiency Virus (HIV),Hepatitis C Virus (HCV), and Hepatitis B Virus (HBV), were processedusing an automated DNA preparation and amplification system (Roche PilotSystem). Eluates from each sample that had undergone the samplepreparation system were collected and distributed (25 μl in each well)into amplification plates for real-time PCR detection using TaqMan®probes. 25 μl of an activated Master Mix (6.6 mM manganese acetate pH6.1, 0.036 μM sodium acetate, 10.8% DMSO, 0.054 μM sodium acetate pH7.0, 240 mM potassium acetate pH 7.0, 6% glycerol, 120 mM Tricine pH8.0, 0.4 U/μL UNG, 800 μM dGTP, 800 μM dATP, 800 μM dCTP, 1600 μM dUTP,1.8 U/μL ZO5-D DNA Polymerase) containing forward and reverse primersand TaqMan® probes with or without N²-benzyl-dG was then added to bringthe final reaction volume to 500 and the plates were sealed andintroduced into the thermocycler. The thermocycling profile wasconducted as shown below in Table 2.

TABLE 2 Acquisition Plateau Measurement Ramp Rate Mode Temperature (C.°) Mode (hh:mm:ss) (hh:mm:ss) (° C./s) Cycles Pre- UNG-Step 50 —00:02:00 00:00:00 2.2 1 PCR UNG/Template 94 — 00:00:05 00:00:00 4.4Denaturating RT-Step 55 — 00:02:00 00:00:00 2.2 60 — 00:06:00 00:00:004.4 65 — 00:04:00 00:00:00 4.4 1. Measurement 95 — 00:00:05 00:00:00 4.45 55 Single 00:00:30 00:00:08 2.2 2. Measurement 91 — 00:00:05 00:00:004.4 45 58 Single 00:00:25 00:00:08 2.2 Cooling 40 — 00:02:00 00:00:002.2 1

Forward and reverse primer sequences used in the experiment ranged infinal concentration between 0.125 μM and 0.3 μM and they were selectedfrom the following. SEQ ID NO: 9 to 24 for HIV Type 1 (HIV-1) GAG; SEQID NO: 25 to 32 for HIV-1 LTR; SEQ ID NO: 33 to 35 for HIV Type 2(HIV-2); SEQ ID NO: 36 and 37 for HBV; SEQ ID NO: 38-59 for HCV.

TaqMan® probe sequences used in the experiment ranged in finalconcentration between 0.15 μM and 0.3 μM and they were selected from thefollowing. SEQ ID NO: 60 to 64 for HIV-1 GAG; SEQ ID NO: 65 and 66 forHIV-1 LTR; SEQ ID NO: 67 for HIV-2; SEQ ID NO: 68 for HBV; SEQ ID NO:69-76 for HCV. All the probes were labeled at the 5′ terminus by afluorescent dye: FAM for the HIV (both HIV-1 and HIV-2) probes, HEX forthe HBV probe, and JA270 for the HCV probe, and contained an internalBHQ-2 quencher molecule.

For TaqMan® probes that contained the N²-benzyl-dG modified nucleotide,an internal deoxyguanosine residue, located approximately in a positionthat is the middle of the probe was modified from dG to N²-benzyl-dG.For example, in the HIV-2 probe (SEQ ID NO: 67), the dG residue atposition 12 from the 5′ terminus was converted to N²-benzyl-dG.Similarly for the HBV probe (SEQ ID NO: 68), N²-benzyl-dG was placed atposition 20 from the 5′ terminus.

The results of the experiment described above for the false positivityreduction by N²-benzyl-dG are as follows. In the assays usingconventional probes (i.e. without N²-benzyl-dG), no FAM signal (fordetection of HIV-1 and HIV-2), one HEX signal (for detection of HBV) and39 JA270 signals (for detection of HCV) were detected out of the 388samples. This lead to a false positivity rate of 10.3% and a specificityof 348/388 or 89.7%. In the assays using N²-benzyl-dG probes, no FAMsignal, one HEX signal and 19 JA270 signals were detected, leading to afalse positivity rate of 5.15% and a specificity of 368/388 or 94.85%.Therefore, incorporation of N²-benzyl-dG in the HCV TaqMan® proberesulted in a 50% reduction of the false positive signal in the JA270channel.

While the invention has been described in detail with reference tospecific examples, it will be apparent to one skilled in the art thatvarious modifications can be made within the scope of this invention.Thus the scope of the invention should not be limited by any of theexamples described herein, but by the claims presented below.

All publications including patent applications and patents cited in thisapplication are incorporated by reference in their entirety for allpurposes to the same extent as if each individual publication wereindividually indicated to be incorporated by reference for all purposes.

1. A method of preventing the extension by DNA polymerase of a primeroligonucleotide that hybridizes to a template nucleotide sequence in anassay employing the extension of a primer in a template-dependent mannercomprising, incorporating a minor groove binder on the templatenucleotide sequence and wherein the primer oligonucleotide is incapableof being extended by more than 2 nucleotides beyond the position of theN²-benzyl-dG nucleotide.
 2. The method of claim 1 wherein the minorgroove binder is a modified nucleotide.
 3. The method of claim 3 whereinsaid modified nucleotide is N²-benzyl-deoxyguanosine (N²-benzyl-dG) 4.The method of claim 1 wherein the assay is selected from the groupconsisting of PCR amplification, DNA sequencing and genotyping.
 5. Themethod of claim 4 wherein the assay is PCR amplification.
 6. A method ofreducing or preventing non-specific amplification of nucleic acid duringan amplification reaction comprising providing at least one pair ofprimer oligonucleotides capable of amplifying a target nucleic acidsequence; providing a probe oligonucleotide that incorporates a minorgroove binder that blocks the extension of the primer oligonucleotide bya DNA polymerase by more than 2 nucleotides beyond the position of themodified nucleotide when the primer oligonucleotide hybridizes to theprobe oligonucleotide.
 7. The method of claim 6 wherein said minorgroove binder is a modified nucleotide
 8. The method of claim 7 whereinsaid modified nucleotide is N²-benzyl-dG.
 9. The method of claim 6wherein the amplification reaction is a Taqman PCR assay and the probeoligonucleotide is a 5′ nuclease probe.
 10. A reaction mixture for theamplification of nucleic acids, comprising at least one pair of primeroligonucleotides and at least one probe oligonucleotide thatincorporates a N²-benzyl-dG nucleotide.
 11. The reaction mixture ofclaim 10 further comprising a nucleotide-incorporating biocatalyst,nucleoside triphosphates, and a buffer suitable for the amplification ofnucleic acids by the nucleotide-incorporating biocatalyst.
 12. A kit forthe amplification of nucleic acids, comprising at least one pair ofprimer oligonucleotides, at least one probe oligonucleotide thatincorporates a N²-benzyl-dG nucleotide, at least onenucleotide-incorporating biocatalyst, nucleoside triphosphates, a buffersuitable for the amplification of nucleic acids by the at least onenucleotide-incorporating biocatalyst, and a set of instructions forperforming the amplification of nucleic acids.
 13. The kit of claim 12further comprising one or more pairs of primer oligonucleotides and oneor more probe oligonucleotides that incorporate a N²-benzyl-dGnucleotide.